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- PDB-9tme: Structure of Plasmodium falciparum Transketolase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9tme
TitleStructure of Plasmodium falciparum Transketolase in complex with Oxythiamine
Componentstransketolase
KeywordsTRANSFERASE / Malaria / inhibitor / transketolase
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / nucleus / cytosol / cytoplasm
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain ...Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.813 Å
AuthorsRaimi, O.G. / Akintola, I.A. / Orogun, Y. / Babalola, K.I. / Soriyan, O.O. / Ogunlana, O.O. / Ogunjimi, A.A. / Vanderpuye, O.A. / Fadare, O.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Plasmodium falciparum Transketolase in complex with Oxythiamine
Authors: Raimi, O.G. / Fadare, A.O.
History
DepositionDec 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: transketolase
B: transketolase
C: transketolase
D: transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,40018
Polymers303,6404
Non-polymers1,76014
Water35,6881981
1
A: transketolase
C: transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,79210
Polymers151,8202
Non-polymers9728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-62 kcal/mol
Surface area42370 Å2
MethodPISA
2
B: transketolase
D: transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,6088
Polymers151,8202
Non-polymers7886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-64 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.388, 142.810, 176.185
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
transketolase / Transferase


Mass: 75910.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_0610800 / Production host: Escherichia coli (E. coli) / References: UniProt: C6KSV3, transketolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-A1JWS / Oxythiamine / 5-[[5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-3-ium-3-yl]methyl]-2-methyl-1H-pyrimidin-6-one


Mass: 266.339 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H16N3O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1981 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2M potassium citrate diabasic monohydrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.81→110.942 Å / Num. obs: 260015 / % possible obs: 99.19 % / Redundancy: 13.7 % / CC1/2: 0.995 / Net I/σ(I): 7.1
Reflection shellResolution: 1.813→1.884 Å / Num. unique obs: 12557 / CC1/2: 0.395

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.813→110.942 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.833 / SU ML: 0.106 / Cross valid method: NONE / ESU R: 0.131 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.217 12987 5.03 %
Rwork0.1809 245224 -
all0.183 --
obs-258211 99.191 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.444 Å2
Baniso -1Baniso -2Baniso -3
1--1.393 Å20 Å20 Å2
2--1.883 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.813→110.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21136 0 112 1981 23229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01321774
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719679
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6429480
X-RAY DIFFRACTIONr_angle_other_deg1.3991.57345935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89852659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2123.8431137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.317153715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7151576
X-RAY DIFFRACTIONr_chiral_restr0.080.22789
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0224383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024397
X-RAY DIFFRACTIONr_nbd_refined0.2070.24617
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.218965
X-RAY DIFFRACTIONr_nbtor_refined0.1690.210608
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.29019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.21615
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2190.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.225
X-RAY DIFFRACTIONr_nbd_other0.1780.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.250
X-RAY DIFFRACTIONr_mcbond_it1.4192.09110635
X-RAY DIFFRACTIONr_mcbond_other1.4192.09110634
X-RAY DIFFRACTIONr_mcangle_it2.0023.13113288
X-RAY DIFFRACTIONr_mcangle_other2.0023.13113289
X-RAY DIFFRACTIONr_scbond_it2.4612.3911139
X-RAY DIFFRACTIONr_scbond_other2.4612.3911140
X-RAY DIFFRACTIONr_scangle_it3.8423.45916190
X-RAY DIFFRACTIONr_scangle_other3.8423.45916191
X-RAY DIFFRACTIONr_lrange_it4.98625.57725281
X-RAY DIFFRACTIONr_lrange_other4.98625.57725282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.813-1.860.4228520.414161630.415190620.5360.54389.26140.411
1.86-1.9110.3539000.345176880.345186400.6490.65699.7210.346
1.911-1.9660.2949530.285171420.285180990.7760.79899.97790.285
1.966-2.0260.2738500.245167580.246176090.8470.85699.99430.239
2.026-2.0930.268690.225161720.227170420.8680.88399.99410.215
2.093-2.1660.2468470.201156880.203165350.8990.9111000.189
2.166-2.2480.237980.186151610.188159590.9160.9251000.172
2.248-2.340.2197500.169146130.171153630.9310.9451000.154
2.34-2.4440.2147860.161139770.164147630.9360.9491000.146
2.444-2.5630.1946980.146134030.148141010.9510.9611000.131
2.563-2.7020.1976450.144128120.146134570.950.9621000.129
2.702-2.8650.2146580.152120500.155127080.9440.9591000.138
2.865-3.0630.1986280.153113730.155120010.9540.9641000.141
3.063-3.3080.2065730.166105970.168111700.950.9581000.157
3.308-3.6240.1975040.16698140.168103180.9580.9661000.16
3.624-4.0510.1764270.14789400.14893670.970.9741000.144
4.051-4.6770.1514490.1278560.12283050.9770.9811000.123
4.677-5.7250.1963480.15767280.15970760.9740.9781000.161
5.725-8.0860.1982730.17852700.17955430.9710.9771000.179
8.086-110.9420.211790.20830200.20831990.9370.9421000.221

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